[BioC] affylmGUI segfault on "pd.ragene.1.0.st.v1"

[Wolfgang Huber]

Hi Harry & Matt

re your second question, about the CDF package: the way the affy package 
works, it expects a package with name "ragene10stv1cdf", containing an 
R-environment of that same name, with the probeset definitions for that 
chip.

Note that the CDF packages that the "affy" package uses are *not* the 
same as the platform design packages that the "oligo" package uses.
Essentially: affy = old, tried and tested, but only works for convential 
Affymetrix genechips for mRNA analysis with genechip using 3' probe sets.
oligo = newer, more general, also suitable for more recent chip types 
inclduding for genotyping..

It seems that you want affy and CDF packages. The make.cdf.package 
function from the makecdfenv package is what you or Matt would want to 
use to build these.

Jim McDonald (cc-ed) has written an overview over the software tools for 
analysing Affymetrix arrays, unfortunately I could not figure out how to 
find it from the Bioconductor webpage, so maybe he can help with that.


Best wishes
  Wolfgang

Harry Mangalam ha scritto:
> Hi All,
> 
> I've been trying to get affylmGUI to run on my laptop (3GB, Ubuntu 
> 8.04, R as below:
> =====
>> sessionInfo()
> R version 2.8.0 (2008-10-20)
> i686-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] tools     tcltk     stats     graphics  grDevices utils     
> datasets
> [8] methods   base
> 
> other attached packages:
> [1] affylmGUI_1.16.0     affy_1.16.0          preprocessCore_1.0.0
> [4] affyio_1.6.1         Biobase_2.2.1        limma_2.16.3
> =====
> The commands to start affylmGUI are:
> library("pd.ragene.1.0.st.v1") # the array set, from Matt Settles
> library("oligo")
> library("affylmGUI")
> affylmGUI()
> 
> when I try to load data, whether my own (or the estrogen data set), it 
> segfaults at the same place:
> After I select a working directory, and select the targets file 
> (included below), [R churns for a few seconds], and give the new data 
> set a name, I can see that the data is 'available' via the data tree 
> in the left panel.
> 
> At the point where I try to view the RNA targets via Menu -> RNA 
> Targets -> RNA Targets, and release the mouse button, it segfaults, 
> leaving the traceback:
> 
> http://moo.nac.uci.edu/~hjm/affylmGUI.traceback
> 
> As I said above, this is the case if it's my data or the estrogen data 
> set.
> 
> If I try to bypass that step and go direct to normalization (with my 
> data), it will eventually emit the error that I don't have the 
> correct CDF environment:
> 
> ==== Error message ====
> Error in getCdfInfo(object): Could not obtain CDF environment, 
> problems encountered: Specified environment does not contain 
> RaGene-1_0-st-v1 Library - package ragene10stv1cdf not installed. 
> Data for package affy did not contain ragene10stv1cdf Bioconductor - 
> ragene10stv1cdf not available
> =======================
> 
> This despite loading without error the correct (from Matt Settles) 
> library beforehand. > library("pd.ragene.1.0.st.v1")
> Does the spelling variant muck it up?  
> 
> Best wishes,
> harry
> 
> 
> ==== targets.txt (whitespaces are TABS) ====
> 
> Name    FileName        Target
> AB.1    0908F-02_AB_1.CEL       AB_Only
> AB.2    0908F-02_AB_2.CEL       AB_Only
> AB.3    0908F-02_AB_3.CEL       AB_Only
> CIQ.1   0908F-02_CIQ_1.CEL      CIQ_Only
> CIQ.2   0908F-02_CIQ_2.CEL      CIQ_Only
> CIQ.3   0908F-02_CIQ_3.CEL      CIQ_Only
> CIQ+AB.1        0908F-02_CIQ_AB_1.CEL   CIQ_AB_CoTreatment
> CIQ+AB.2        0908F-02_CIQ_AB_2.CEL   CIQ_AB_CoTreatment
> CIQ+AB.3        0908F-02_CIQ_AB_3.CEL   CIQ_AB_CoTreatment
> Untreated.1     0908F-02_Untreated_1.CEL        CONTROL
> Untreated.2     0908F-02_Untreated_2.CEL        CONTROL
> Untreated.3     0908F-02_Untreated_3.CEL        CONTROL
>